From 82754f40d717343298581289e097fc5bac5153a7 Mon Sep 17 00:00:00 2001 From: Tabassum Kakar Date: Thu, 2 Jan 2025 17:09:14 -0500 Subject: [PATCH 1/4] Expanded readmes for each container --- containers/anndata-to-ui/README.md | 18 ++++++- containers/anndata-to-ui/context/main.py | 2 +- containers/h5ad-to-arrow/README.md | 15 ++++++ containers/mudata-to-ui/README.md | 15 +++++- containers/ome-tiff-offsets/README.md | 17 +++++- containers/ome-tiff-segments/README.md | 23 +++++++- .../text-output/output_ome/aoi.zarr/.zattrs | 4 -- .../text-output/output_ome/aoi.zarr/.zgroup | 3 -- .../output_ome/aoi.zarr/layers/.zattrs | 4 -- .../output_ome/aoi.zarr/layers/.zgroup | 3 -- .../output_ome/aoi.zarr/obs/.zattrs | 10 ---- .../output_ome/aoi.zarr/obs/.zgroup | 3 -- .../output_ome/aoi.zarr/obs/aoi_id/.zarray | 24 --------- .../output_ome/aoi.zarr/obs/aoi_id/.zattrs | 4 -- .../output_ome/aoi.zarr/obs/aoi_id/0 | Bin 42 -> 0 bytes .../aoi.zarr/obs/aoi_id_numeric/.zarray | 24 --------- 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It also -selects an approriate subset of genes to be used for visualization. \ No newline at end of file +This container saves [an AnnData store](https://anndata.readthedocs.io/en/latest/anndata.read_h5ad.html) in `zarr` format for viewing in the browser due to it's scalability, performance, and flexibility. It also selects an appropriate subset of genes to be used for visualization. + +## Input +The input to the container is an [AnnData file in h5ad format](https://anndata.readthedocs.io/en/latest/anndata.read_h5ad.html). + + +## Output +The output is the converted `zarr` store. + + +## Normalization +All data from the input is scaled to zero-mean unit-variance ( # https://github.com/hubmapconsortium/salmon-rnaseq/blob/master/bin/analysis/scanpy_entry_point.py#L47) #####--- update line number in the link. +The `X` is replaced with the log-normalized raw counts to be visualized by Vitessce. + +## Example +Example of a hubmap dataset using this container for data conversion would be `HBM856.HVWM.567` \ No newline at end of file diff --git a/containers/anndata-to-ui/context/main.py b/containers/anndata-to-ui/context/main.py index 2cc2ad0..97027be 100644 --- a/containers/anndata-to-ui/context/main.py +++ b/containers/anndata-to-ui/context/main.py @@ -53,7 +53,7 @@ def main(input_dir, output_dir): # All data from secondary_analysis is scaled at the moment to zero-mean unit-variance # https://github.com/hubmapconsortium/salmon-rnaseq/blob/master/bin/analysis/scanpy_entry_point.py#L47 - # We currently cannot visaulize this in Vitessce so we replace `X` with the log-normalized raw counts: + # We currently cannot visualize this in Vitessce so we replace `X` with the log-normalized raw counts: # https://github.com/hubmapconsortium/salmon-rnaseq/commit/9cf1dd4dbe4538b565a0355f56399d3587827eff # Ideally, we should be able to manage the `layers` and `X` simultaneously in `zarr` but currently we cannot: # https://github.com/theislab/anndata/issues/524 diff --git a/containers/h5ad-to-arrow/README.md b/containers/h5ad-to-arrow/README.md index bfb5e3a..4acc36a 100644 --- a/containers/h5ad-to-arrow/README.md +++ b/containers/h5ad-to-arrow/README.md @@ -2,3 +2,18 @@ This container translates [anndata's h5ad](https://anndata.readthedocs.io/en/latest/anndata.read_h5ad.html) to [Apache Arrow](https://arrow.apache.org/), as well as CSV, and Vitessce JSON which conforms to our [schemas](https://github.com/hubmapconsortium/vitessce/tree/master/src/schemas). +The arrow format is a columnar format optimized for analytical workloads like querying and aggregations and is faster than AnnData's row-based storage for certain operations. + +## Input +The input to the container is an [an AnnData file in h5ad format](https://anndata.readthedocs.io/en/latest/anndata.read_h5ad.html). + + +## Output +The output includes the converted `arrow` file, a csv file representing the arrow file for readability purposes, and json files representing cells and cell sets crucial for Vitessce visualization. + + +## Normalization +None + +## Example +Example of a hubmap dataset using this container for data conversion for Vitessce (visualization) would be `HBM768.NCSB.762` diff --git a/containers/mudata-to-ui/README.md b/containers/mudata-to-ui/README.md index 773c267..d35b794 100644 --- a/containers/mudata-to-ui/README.md +++ b/containers/mudata-to-ui/README.md @@ -2,4 +2,17 @@ This container saves [a MuData store](https://mudata.readthedocs.io/en/latest/api/generated/mudata.read_h5mu.html#mudata.read_h5mu) in `zarr` format for viewing in the browser. -It also selects an approriate subset of genes to be used for visualization and generates genomic profiles for all the present clusterings. \ No newline at end of file +It also selects an appropriate subset of genes to be used for visualization and generates genomic profiles for all the present clusters. + +## Input +The input to the container is an [AnnData file in h5ad format](https://anndata.readthedocs.io/en/latest/anndata.read_h5ad.html). + +## Output +The output is the converted zarr store. + +## Normalization +All data from the input is scaled to zero-mean unit-variance ( # https://github.com/hubmapconsortium/salmon-rnaseq/blob/master/bin/analysis/scanpy_entry_point.py#L47) #####--- update line number in the link. +The `X` is replaced with the log-normalized raw counts to be visualized by Vitessce. + +## Example +Example of a hubmap dataset using this container for data conversion for Vitessce (visualization) would be `HBM768.NCSB.762` diff --git a/containers/ome-tiff-offsets/README.md b/containers/ome-tiff-offsets/README.md index aa6dff5..c685d07 100644 --- a/containers/ome-tiff-offsets/README.md +++ b/containers/ome-tiff-offsets/README.md @@ -1,3 +1,18 @@ # ome-tiff-offsets -This docker container creates a JSON list of byte offsets for each TIFF from an input directory. This makes visualization much more efficient as we can request specific IFDs and their tiles more efficiently +This docker container creates a JSON list of byte offsets for each TIFF from an input directory. This is needed for visualizing image datasets as it makes visualization much more efficient by allowing requesting specific IFDs and their tiles more efficiently. + +## Input +The input to the container is one or more ome-tiff image files. + + +## Output +The output is a json file that includes an array/list of byte offsets for every input ome-tiff image. + + +## Normalization +None + +## Example +Example of a hubmap dataset using this container for offsets generation for Vitessce (visualization) would be `HBM974.DMWR.753`. + diff --git a/containers/ome-tiff-segments/README.md b/containers/ome-tiff-segments/README.md index 439be6d..a8411f7 100644 --- a/containers/ome-tiff-segments/README.md +++ b/containers/ome-tiff-segments/README.md @@ -1,3 +1,24 @@ # ome-tiff-segments +This container creates different component datasets needed for the visualization of GeoMx Assays Ome-tiff files which includes regions of interests (ROIs) and Areas of Interests (AOI). These datasets are created by converting the ome-tiff to an ome-xml file. -This container creates different component datasets needed for the visualization of GeoMx Assays Ome-tiff files. \ No newline at end of file + +## Input +The input to the container is the ome-tiff file from GeoMx assay. + +## Output +The following output files are generated to support the visualization of GeoMx assays. + +- ROIs as `obsSegmentations.json` file by extracting the vertices from Polygon tags within each ROI. + +- A Segmentation OME-TIFF file extracted from the bitmask within each ROI’s mask and grouped by the segment (text field within the mask). + +- AOIs as Zarr store with obs representing the segment, roi-id, and aoi-id. The aoi-id has composite values (e.g., Shape:2), so the index is the numeric part extracted from this composite value. + +- ROIs as Zarr store with obs having channel thresholds for the ROIs extracted from the annotations in ome-xml. + + +## Normalization +None + +## Example +Example of a hubmap dataset using this container for data conversion would be `TO DO` \ No newline at end of file diff --git a/containers/ome-tiff-segments/text-output/output_ome/aoi.zarr/.zattrs b/containers/ome-tiff-segments/text-output/output_ome/aoi.zarr/.zattrs deleted file mode 100644 index 82ba51b..0000000 --- a/containers/ome-tiff-segments/text-output/output_ome/aoi.zarr/.zattrs +++ /dev/null @@ -1,4 +0,0 @@ -{ - "encoding-type": "anndata", - "encoding-version": "0.1.0" -} \ No newline at end of file diff --git a/containers/ome-tiff-segments/text-output/output_ome/aoi.zarr/.zgroup b/containers/ome-tiff-segments/text-output/output_ome/aoi.zarr/.zgroup deleted file mode 100644 index 3b7daf2..0000000 --- a/containers/ome-tiff-segments/text-output/output_ome/aoi.zarr/.zgroup +++ /dev/null @@ -1,3 +0,0 @@ -{ - "zarr_format": 2 -} \ No newline at end of file diff --git a/containers/ome-tiff-segments/text-output/output_ome/aoi.zarr/layers/.zattrs b/containers/ome-tiff-segments/text-output/output_ome/aoi.zarr/layers/.zattrs deleted file mode 100644 index a204673..0000000 --- a/containers/ome-tiff-segments/text-output/output_ome/aoi.zarr/layers/.zattrs +++ /dev/null @@ -1,4 +0,0 @@ -{ - "encoding-type": "dict", - "encoding-version": "0.1.0" -} \ No newline at end of file diff --git a/containers/ome-tiff-segments/text-output/output_ome/aoi.zarr/layers/.zgroup b/containers/ome-tiff-segments/text-output/output_ome/aoi.zarr/layers/.zgroup deleted file mode 100644 index 3b7daf2..0000000 --- a/containers/ome-tiff-segments/text-output/output_ome/aoi.zarr/layers/.zgroup +++ /dev/null @@ -1,3 +0,0 @@ -{ - "zarr_format": 2 -} \ No newline at end of file diff --git a/containers/ome-tiff-segments/text-output/output_ome/aoi.zarr/obs/.zattrs b/containers/ome-tiff-segments/text-output/output_ome/aoi.zarr/obs/.zattrs deleted file mode 100644 index 0aba6b1..0000000 --- a/containers/ome-tiff-segments/text-output/output_ome/aoi.zarr/obs/.zattrs +++ /dev/null @@ -1,10 +0,0 @@ -{ - "_index": "aoi_id_numeric", - "column-order": [ - "aoi_id", - "roi_id", - "segment" - ], - "encoding-type": "dataframe", - "encoding-version": "0.2.0" -} \ No newline at end of file diff --git a/containers/ome-tiff-segments/text-output/output_ome/aoi.zarr/obs/.zgroup b/containers/ome-tiff-segments/text-output/output_ome/aoi.zarr/obs/.zgroup deleted file mode 100644 index 3b7daf2..0000000 --- a/containers/ome-tiff-segments/text-output/output_ome/aoi.zarr/obs/.zgroup +++ /dev/null @@ -1,3 +0,0 @@ -{ - "zarr_format": 2 -} \ No newline at end of file diff --git a/containers/ome-tiff-segments/text-output/output_ome/aoi.zarr/obs/aoi_id/.zarray b/containers/ome-tiff-segments/text-output/output_ome/aoi.zarr/obs/aoi_id/.zarray deleted file mode 100644 index eca134e..0000000 --- a/containers/ome-tiff-segments/text-output/output_ome/aoi.zarr/obs/aoi_id/.zarray +++ /dev/null @@ -1,24 +0,0 @@ -{ - "chunks": [ - 2 - ], - "compressor": { - "blocksize": 0, - "clevel": 5, - "cname": "lz4", - "id": "blosc", - "shuffle": 1 - }, - "dtype": "|O", - "fill_value": 0, - "filters": [ - { - "id": "vlen-utf8" - } - ], - "order": "C", - "shape": [ - 2 - ], - "zarr_format": 2 -} \ No newline at end of file diff --git a/containers/ome-tiff-segments/text-output/output_ome/aoi.zarr/obs/aoi_id/.zattrs b/containers/ome-tiff-segments/text-output/output_ome/aoi.zarr/obs/aoi_id/.zattrs deleted file mode 100644 index 6e14470..0000000 --- a/containers/ome-tiff-segments/text-output/output_ome/aoi.zarr/obs/aoi_id/.zattrs +++ /dev/null @@ -1,4 +0,0 @@ -{ - "encoding-type": "string-array", - "encoding-version": "0.2.0" -} \ No newline at end of file diff --git a/containers/ome-tiff-segments/text-output/output_ome/aoi.zarr/obs/aoi_id/0 b/containers/ome-tiff-segments/text-output/output_ome/aoi.zarr/obs/aoi_id/0 deleted file mode 100644 index 3601f82f5b65811f781d77ba68f06819450cb753..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 42 hcmZQ#G-i}yU|;}YEg)tBVs;=7&PXgswK765O#wuG1!DjJ diff --git a/containers/ome-tiff-segments/text-output/output_ome/aoi.zarr/obs/aoi_id_numeric/.zarray b/containers/ome-tiff-segments/text-output/output_ome/aoi.zarr/obs/aoi_id_numeric/.zarray deleted file mode 100644 index eca134e..0000000 --- a/containers/ome-tiff-segments/text-output/output_ome/aoi.zarr/obs/aoi_id_numeric/.zarray +++ /dev/null @@ -1,24 +0,0 @@ -{ - "chunks": [ - 2 - ], - "compressor": { - "blocksize": 0, - "clevel": 5, - "cname": "lz4", - "id": "blosc", - "shuffle": 1 - }, - "dtype": "|O", - "fill_value": 0, - "filters": [ - { - "id": "vlen-utf8" - } - ], - "order": "C", - "shape": [ - 2 - ], - "zarr_format": 2 -} \ No newline at end of file diff --git a/containers/ome-tiff-segments/text-output/output_ome/aoi.zarr/obs/aoi_id_numeric/.zattrs b/containers/ome-tiff-segments/text-output/output_ome/aoi.zarr/obs/aoi_id_numeric/.zattrs deleted file mode 100644 index 6e14470..0000000 --- a/containers/ome-tiff-segments/text-output/output_ome/aoi.zarr/obs/aoi_id_numeric/.zattrs +++ /dev/null @@ -1,4 +0,0 @@ -{ - "encoding-type": "string-array", - "encoding-version": "0.2.0" -} \ No newline at end of file diff --git a/containers/ome-tiff-segments/text-output/output_ome/aoi.zarr/obs/aoi_id_numeric/0 b/containers/ome-tiff-segments/text-output/output_ome/aoi.zarr/obs/aoi_id_numeric/0 deleted file mode 100644 index 4b76651c8c6afefcce63015b36ab8fe503f97e15..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 30 bcmZQ#G-l*uU|;}YIUr^NVn!e~0uiPF3~m73 diff --git a/containers/ome-tiff-segments/text-output/output_ome/aoi.zarr/obs/roi_id/.zarray b/containers/ome-tiff-segments/text-output/output_ome/aoi.zarr/obs/roi_id/.zarray deleted file mode 100644 index eca134e..0000000 --- a/containers/ome-tiff-segments/text-output/output_ome/aoi.zarr/obs/roi_id/.zarray +++ /dev/null @@ -1,24 +0,0 @@ -{ - 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It also selects an appropriate subset of genes to be used for visualization. +This container saves [an AnnData store](https://anndata.readthedocs.io/en/latest/anndata.read_h5ad.html) in `zarr` format for viewing in the browser due to it's scalability, performance, and flexibility features. It also selects an appropriate subset of genes to be used for visualization. ## Input The input to the container is an [AnnData file in h5ad format](https://anndata.readthedocs.io/en/latest/anndata.read_h5ad.html). @@ -11,7 +11,7 @@ The output is the converted `zarr` store. ## Normalization -All data from the input is scaled to zero-mean unit-variance ( # https://github.com/hubmapconsortium/salmon-rnaseq/blob/master/bin/analysis/scanpy_entry_point.py#L47) #####--- update line number in the link. +All data from the input is scaled to [zero-mean unit-variance] (https://github.com/hubmapconsortium/salmon-rnaseq/blob/master/bin/analysis/scanpy_entry_point.py#L47) `TODO: update line number in the link`. The `X` is replaced with the log-normalized raw counts to be visualized by Vitessce. ## Example diff --git a/containers/h5ad-to-arrow/README.md b/containers/h5ad-to-arrow/README.md index 4acc36a..7dad50b 100644 --- a/containers/h5ad-to-arrow/README.md +++ b/containers/h5ad-to-arrow/README.md @@ -5,11 +5,11 @@ as well as CSV, and Vitessce JSON which conforms to our [schemas](https://github The arrow format is a columnar format optimized for analytical workloads like querying and aggregations and is faster than AnnData's row-based storage for certain operations. ## Input -The input to the container is an [an AnnData file in h5ad format](https://anndata.readthedocs.io/en/latest/anndata.read_h5ad.html). +The input to the container is an [annData file in h5ad format](https://anndata.readthedocs.io/en/latest/anndata.read_h5ad.html). ## Output -The output includes the converted `arrow` file, a csv file representing the arrow file for readability purposes, and json files representing cells and cell sets crucial for Vitessce visualization. +The output includes the converted `arrow` file, a csv file representing the arrow file for readability purposes, and json files representing cells and cell sets for Vitessce. ## Normalization diff --git a/containers/mudata-to-ui/README.md b/containers/mudata-to-ui/README.md index d35b794..cf47c99 100644 --- a/containers/mudata-to-ui/README.md +++ b/containers/mudata-to-ui/README.md @@ -11,7 +11,7 @@ The input to the container is an [AnnData file in h5ad format](https://anndata.r The output is the converted zarr store. ## Normalization -All data from the input is scaled to zero-mean unit-variance ( # https://github.com/hubmapconsortium/salmon-rnaseq/blob/master/bin/analysis/scanpy_entry_point.py#L47) #####--- update line number in the link. +All data from the input is scaled to [zero-mean unit-variance] (https://github.com/hubmapconsortium/salmon-rnaseq/blob/master/bin/analysis/scanpy_entry_point.py#L47) `TODO: update line number in the link`. The `X` is replaced with the log-normalized raw counts to be visualized by Vitessce. ## Example diff --git a/containers/ome-tiff-segments/README.md b/containers/ome-tiff-segments/README.md index a8411f7..3d6e920 100644 --- a/containers/ome-tiff-segments/README.md +++ b/containers/ome-tiff-segments/README.md @@ -10,7 +10,7 @@ The following output files are generated to support the visualization of GeoMx a - ROIs as `obsSegmentations.json` file by extracting the vertices from Polygon tags within each ROI. -- A Segmentation OME-TIFF file extracted from the bitmask within each ROI’s mask and grouped by the segment (text field within the mask). +- A Segmentation OME-TIFF file extracted from the Bitmask within each ROI’s mask and grouped by the segment (text field within the mask). - AOIs as Zarr store with obs representing the segment, roi-id, and aoi-id. The aoi-id has composite values (e.g., Shape:2), so the index is the numeric part extracted from this composite value. @@ -21,4 +21,4 @@ The following output files are generated to support the visualization of GeoMx a None ## Example -Example of a hubmap dataset using this container for data conversion would be `TO DO` \ No newline at end of file +Example of a hubmap dataset using this container for data conversion would be `Not ingested yet` \ No newline at end of file diff --git a/containers/sprm-to-json/README.md b/containers/sprm-to-json/README.md index f985338..a6aa72a 100644 --- a/containers/sprm-to-json/README.md +++ b/containers/sprm-to-json/README.md @@ -15,4 +15,4 @@ The output includes json files for cells and cell-sets that conform to Vitessce None ## Example -Example of a hubmap dataset using this container for data conversion would be `TO DO` \ No newline at end of file +Example of a hubmap dataset using this container for data conversion would be `TODO` \ No newline at end of file From 357843ff805fd77a19eaf0324936d47db77030ea Mon Sep 17 00:00:00 2001 From: Tabassum Kakar Date: Fri, 3 Jan 2025 10:52:52 -0500 Subject: [PATCH 3/4] Consistent breaks --- containers/ome-tiff-segments/README.md | 2 -- 1 file changed, 2 deletions(-) diff --git a/containers/ome-tiff-segments/README.md b/containers/ome-tiff-segments/README.md index 3d6e920..3679246 100644 --- a/containers/ome-tiff-segments/README.md +++ b/containers/ome-tiff-segments/README.md @@ -1,7 +1,6 @@ # ome-tiff-segments This container creates different component datasets needed for the visualization of GeoMx Assays Ome-tiff files which includes regions of interests (ROIs) and Areas of Interests (AOI). These datasets are created by converting the ome-tiff to an ome-xml file. - ## Input The input to the container is the ome-tiff file from GeoMx assay. @@ -16,7 +15,6 @@ The following output files are generated to support the visualization of GeoMx a - ROIs as Zarr store with obs having channel thresholds for the ROIs extracted from the annotations in ome-xml. - ## Normalization None From 791f0f12c0bda385f257ce43e3b1a20e7e5e7679 Mon Sep 17 00:00:00 2001 From: Tabassum Kakar Date: Fri, 3 Jan 2025 12:04:00 -0500 Subject: [PATCH 4/4] Fixed minor line breaks --- containers/anndata-to-ui/README.md | 2 -- containers/h5ad-to-arrow/README.md | 2 -- containers/ome-tiff-offsets/README.md | 2 -- containers/scatac-csv-to-arrow/README.md | 3 --- containers/seg-mudata-to-zarr/README.md | 2 -- containers/sprm-to-anndata/README.md | 5 +---- containers/sprm-to-json/README.md | 3 --- 7 files changed, 1 insertion(+), 18 deletions(-) diff --git a/containers/anndata-to-ui/README.md b/containers/anndata-to-ui/README.md index e4242aa..2d27d36 100644 --- a/containers/anndata-to-ui/README.md +++ b/containers/anndata-to-ui/README.md @@ -5,11 +5,9 @@ This container saves [an AnnData store](https://anndata.readthedocs.io/en/latest ## Input The input to the container is an [AnnData file in h5ad format](https://anndata.readthedocs.io/en/latest/anndata.read_h5ad.html). - ## Output The output is the converted `zarr` store. - ## Normalization All data from the input is scaled to [zero-mean unit-variance] (https://github.com/hubmapconsortium/salmon-rnaseq/blob/master/bin/analysis/scanpy_entry_point.py#L47) `TODO: update line number in the link`. The `X` is replaced with the log-normalized raw counts to be visualized by Vitessce. diff --git a/containers/h5ad-to-arrow/README.md b/containers/h5ad-to-arrow/README.md index 7dad50b..e86a846 100644 --- a/containers/h5ad-to-arrow/README.md +++ b/containers/h5ad-to-arrow/README.md @@ -7,11 +7,9 @@ The arrow format is a columnar format optimized for analytical workloads like qu ## Input The input to the container is an [annData file in h5ad format](https://anndata.readthedocs.io/en/latest/anndata.read_h5ad.html). - ## Output The output includes the converted `arrow` file, a csv file representing the arrow file for readability purposes, and json files representing cells and cell sets for Vitessce. - ## Normalization None diff --git a/containers/ome-tiff-offsets/README.md b/containers/ome-tiff-offsets/README.md index c685d07..c449726 100644 --- a/containers/ome-tiff-offsets/README.md +++ b/containers/ome-tiff-offsets/README.md @@ -5,11 +5,9 @@ This docker container creates a JSON list of byte offsets for each TIFF from an ## Input The input to the container is one or more ome-tiff image files. - ## Output The output is a json file that includes an array/list of byte offsets for every input ome-tiff image. - ## Normalization None diff --git a/containers/scatac-csv-to-arrow/README.md b/containers/scatac-csv-to-arrow/README.md index e63e04e..6f8320f 100644 --- a/containers/scatac-csv-to-arrow/README.md +++ b/containers/scatac-csv-to-arrow/README.md @@ -2,15 +2,12 @@ This container takes the CSV from the [HuBMAP scATAC-seq pipeline](https://github.com/hubmapconsortium/sc-atac-seq-pipeline) and converts it to [Apache Arrow](https://arrow.apache.org/), as well as a normalized CSV, and Vitessce JSON which conforms to our [schemas](https://github.com/hubmapconsortium/vitessce/tree/master/src/schemas). - ## Input The input to the container is a csv file. - ## Output The output is an arrow file, along with csv and json files representing cells and cell sets for Vitessce. - ## Normalization To be continue... diff --git a/containers/seg-mudata-to-zarr/README.md b/containers/seg-mudata-to-zarr/README.md index df9367d..e7da47f 100644 --- a/containers/seg-mudata-to-zarr/README.md +++ b/containers/seg-mudata-to-zarr/README.md @@ -6,11 +6,9 @@ For Vitessce, the index of the zarr store needs to be a number so that it can be ## Input The input to the container is an [MuData store](https://anndata.readthedocs.io/en/latest/anndata.read_h5ad.html). - ## Output The output includes the converted `zarr` store for each of the mask name present in the `mudata` as well as `metadata.json` file that includes the mask names needed to retrieve the corresponding zarr files for visualization. - ## Normalization The compound index from the mudata is transformed into numeric index by extracting the numeric part from it. diff --git a/containers/sprm-to-anndata/README.md b/containers/sprm-to-anndata/README.md index 7471a49..7ac84dc 100644 --- a/containers/sprm-to-anndata/README.md +++ b/containers/sprm-to-anndata/README.md @@ -2,15 +2,12 @@ This container takes [SPRM](https://docs.google.com/document/d/1c7UR0Pe1newpVhQY2HEFkfV8O7GAj9Vk4XnuSiSnDeY/edit) output CSVs and converts them into an [AnnData zarr store](https://anndata.readthedocs.io/en/latest/anndata.AnnData.write_zarr.html#anndata.AnnData.write_zarr). - ## Input -The input to the container SPRM output csvs. - +The input to the container are SPRM output csvs. ## Output The output of the container is the zarr store created from all the input csv files. - ## Normalization None diff --git a/containers/sprm-to-json/README.md b/containers/sprm-to-json/README.md index a6aa72a..5ea8029 100644 --- a/containers/sprm-to-json/README.md +++ b/containers/sprm-to-json/README.md @@ -2,15 +2,12 @@ This container takes [SPRM](https://docs.google.com/document/d/1c7UR0Pe1newpVhQY2HEFkfV8O7GAj9Vk4XnuSiSnDeY/edit) output CSVs and converts them into Vitessce JSON which conforms to our [schemas](https://github.com/hubmapconsortium/vitessce/tree/master/src/schemas). - ## Input The input to the container SPRM output csvs. - ## Output The output includes json files for cells and cell-sets that conform to Vitessce schemas. - ## Normalization None